dbSNP rs8109507: CYP2G1P:n.1058-6365C>A (chr19-40905329-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000651727.1(CYP2G1P):n.1058-6365C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,184 control chromosomes in the GnomAD database, including 248 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.054 ( 248 hom., cov: 31)

Consequence

CYP2G1P
ENST00000651727.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0110

Publications

0 publications found

Variant links:

Genes affected

CYP2G1P (HGNC:):

CYP2G1P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CYP2G1P	ENST00000651727.1 link	n.1058-6365C>A	intron_variant	Intron 1 of 1
ENSG00000297278	ENST00000746757.1 link	n.100-2979C>A	intron_variant	Intron 1 of 1
ENSG00000297319	ENST00000747088.1 link	n.-190G>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8230

AN:

152066

Hom.:

247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0531

Gnomad AMI

AF:

0.0890

Gnomad AMR

AF:

0.0553

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0159

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0618

Gnomad OTH

AF:

0.0699

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0541

AC:

8226

AN:

152184

Hom.:

248

Cov.:

AF XY:

0.0507

AC XY:

3774

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0530

AC:

2202

AN:

41512

American (AMR)

AF:

0.0552

AC:

843

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0956

AC:

332

AN:

3472

East Asian (EAS)

AF:

0.000771

AC:

AN:

5188

South Asian (SAS)

AF:

0.0441

AC:

213

AN:

4826

European-Finnish (FIN)

AF:

0.0159

AC:

169

AN:

10600

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0618

AC:

4203

AN:

67994

Other (OTH)

AF:

0.0687

AC:

145

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

405

811

1216

1622

2027

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0580

Hom.:

143

Bravo

AF:

0.0564

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.3

(source)

DANN

Benign

0.23

PhyloP100

0.011

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over